Phage’s deep pockets
Weizmann Institute researchers have identified three new families of proteins that viruses use to disrupt bacterial immune signaling
The genomes of phages – viruses that infect bacteria – are largely composed of “dark matter”: genes that encode proteins whose functions remain unknown. Less than four years ago, a team led by Prof. Rotem Sorek at the Weizmann Institute of Science identified a new type of protein within this viral dark matter and dubbed it a “sponge.” Viral sponge proteins are porous and specialize in trapping molecules within deep pockets – much like a sponge that absorbs water. For phages, however, this sponge serves as a weapon: It traps communication molecules that are essential to bacterial immune systems, allowing the phage to take control of the bacterium and multiply inside it unhindered.
Until recently, very few sponge proteins had been found. Their genetic sequences differ greatly from one another, making them difficult to detect. Now, using an innovative research approach that combines artificial intelligence with experimental biology, researchers in Sorek’s lab have uncovered new families of sponge proteins that disrupt immune communication in bacteria. The findings, published in Science, reveal how viruses silence the immune system’s alarm signals, and shed light on the importance of communication disruption in the billion-year-long war between viruses and bacteria.
In the new study, the researchers examined the structures of sponge proteins identified so far and noticed a recurring architectural pattern that could be used to discover new proteins of this type. “They are all small, composed of several identical subunits and contain deep pockets,” explains Sorek. “These pockets carry a positive electrical charge, allowing them to absorb immune alarm molecules, which are typically negatively charged.”
Insights like these used to have limited practical value, but the AI revolution has changed that. “We realized that with advanced AI tools such as Google’s AlphaFold, we could scan an enormous number of proteins and search for those with positively charged pockets capable of trapping immune molecules,” says Dr. Nitzan Tal, who led the new study in Sorek’s lab. “This allowed us to reveal new functions of phage proteins based solely on their structure.”
The scientists scanned a database of 32 million genes encoding phage proteins, from 2 million phage genomes, and used AlphaFold to predict their three-dimensional structures. “We found more than 120 candidates whose structures matched our criteria, and moved on to experimental testing,” says Tal.
The researchers then tested the effectiveness of each candidate against five bacterial immune systems, using a new method developed by research student Jeremy Garb in Sorek’s lab. The approach enabled the team to perform all the tests simultaneously rather than conducting hundreds of separate experiments. These experiments revealed a new family of sponge proteins that the researchers named Lockin. The AI model predicted that these proteins should consist of six identical subunits arranged in a circular structure resembling flower petals. In collaboration with Prof. Philip J. Kranzusch’s team at the Dana-Farber Cancer Institute in Boston, the researchers determined the structure of one family member using X-ray crystallography, confirming the prediction and deciphering exactly how the immune alarm molecule is captured.
“The huge database of viral proteins we analyzed was mostly obtained from sequencing environmental DNA samples that include a large mixture of phages,” says Sorek. “This allowed us to discover the Lockin proteins, which appeared in hundreds of phages that have never been isolated in the lab.”
Along with AI-based predictions, the researchers used additional innovative strategies. “Romi Hadary, another research student in my lab, noticed that genes that encoded known sponge proteins tend to be fused together in phage genomes,” explains Sorek. “This insight allowed us to identify an additional family of sponge proteins, called Sequestin, based on the fact that their genes are fused to those of known sponges. It goes to show that, even in the age of artificial intelligence, there is still great value in the keen observations of human scientists.”
Yet another protein family discovered in the study, called Acb5, initially puzzled the researchers. “These proteins were very similar to sponge proteins, but we discovered that they not only trap alarm molecules – they also cut them,” says Tal. “This was surprising because they didn’t have the structural features typical of molecular cutting tools. This discovery shows how systematic structural scanning can overturn previous scientific assumptions.”
The protein families identified in this study appear in the genomes of thousands of different phages in nature. The researchers also found that a single phage can carry a broad arsenal of sponges and enzymes that neutralize immune alarm molecules. Together, these findings show that proteins disrupting immune communication give phages a significant advantage in their arms race with bacteria.
“It’s not yet known whether viruses that infect plants, animals and humans also use sponge proteins, but the computational and experimental approach we developed makes it possible to test this,” adds Sorek. “If they do, sponge proteins could become targets for the development of antiviral therapies in the future. Our discovery method doesn’t require prior knowledge of protein function, and it doesn’t rely on spotting similarities in genetic sequences or on growing viruses in the lab. It is therefore a powerful tool for uncovering additional immune-related proteins that share structural patterns.”
Also participating in the study were: Dr. Ilya Osterman, Dr. Gil Amitai, Erez Yirmiya, Dr. Nathalie Béchon, Dr. Dina Hochhauser and Barak Madhala from Weizmann’s Molecular Genetics Department; Renee B. Chang and Miguel López Rivera from the Dana-Farber Cancer Institute, Boston, MA; Roy Jacobson from Weizmann’s Plant and Environmental Sciences Department; Dr. Moshe Goldsmith from Weizmann’s Biomolecular Sciences Department; and Dr. Tanita Wein from Weizmann’s Systems Immunology Department.
Prof. Rotem Sorek’s research is supported by Magnus Konow in honor of his mother Olga Konow Rappaport.
Journal
Science
Article Title
Structural modeling reveals phage proteins that manipulate bacterial immune signaling
Singapore researchers advance phage therapy in fight against antimicrobial resistance
New study identifies how Mycobacterium abscessus evades treatment and proposes a strategy to overcome resistance
image:
Findings from A*STAR IDL, NTU Singapore, and NUS provide actionable design principles for more durable phage cocktails, supporting global efforts to develop new countermeasures against drug-resistant infections.
view moreCredit: 123RF
SINGAPORE – Scientists from A*STAR Infectious Diseases Labs (A*STAR IDL), Nanyang Technological University, Singapore’s Lee Kong Chian School of Medicine (LKCMedicine), the National University of Singapore (NUS), and international collaborators have uncovered how Mycobacterium abscessus – a bacterium that causes serious lung infections – can evade bacteriophage (phage) therapy, and demonstrated a combination strategy to overcome this resistance, offering a pathway towards more effective and durable treatments. The study was published in the Proceedings of the National Academy of Sciences.
Antimicrobial resistance (AMR) is an escalating health challenge that is expected to place growing strain on healthcare systems worldwide. As AMR continues to erode the effectiveness of existing antibiotics – with one in six bacterial infections worldwide now resistant to antibiotics – scientists are accelerating efforts to develop new countermeasures such as phage therapy, which uses viruses to target bacteria. These efforts are important for strengthening global health and infectious disease preparedness.
Understanding How Bacteria Adapt to Survive Treatment
M. abscessus infections are challenging to treat due to their intrinsic resistance to many antibiotics and are increasingly recognised as a significant public health threat.
The researchers found that “smooth” strains of M. abscessus, which are more commonly observed in Asia, respond to phage therapy by switching to a “rough” form, both in the laboratory and pre-clinical models. This transition is linked to mutations in genes responsible for producing glycopeptidolipids, which shape the bacteria’s outer surface.
In other cases, the bacteria resisted phage attack without changing form, instead developing mutations in different surface‑related genes, revealing multiple pathways to resistance.
The team uncovered this resistance mechanism while generating phage‑resistant bacterial mutants to investigate phage‑bacteria interactions.
“These findings reveal an important challenge in developing phage‑based therapies. Although phages can effectively eliminate bacteria, they may also inadvertently make infections more difficult to treat, as seen in the ‘rough’ form,” explained Professor Pablo Bifani, senior author and scientist at LKCMedicine.
Designing More Effective Phage Treatments to Treat AMR Infections
To address this, the team developed a combination therapy targeting both the original “smooth” bacteria and the emerging “rough” variants. This two‑pronged approach proved more effective than a single-phage treatment, pointing toward more robust and longer‑lasting phage therapies for patients.
“What started as a straightforward goal: finding phages that can target M. abscessus smooth strains, led us to the discovery of a clinically relevant resistance mechanism,” said Dr Liew Jun Hao, first author and scientist at A*STAR IDL.
“Phage therapy holds great promise as an alternative treatment for AMR infections, and our findings show that how these treatments are designed is critical. By identifying these ‘escape states’, our study underscores the need for the field to systematically account for bacterial adaptation, so that strategies to counter phage resistance can be built into therapies from the outset, as the threat of AMR continues to grow.”
Associate Professor Albert Yick Hou Lim, Senior Consultant in Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, who was not part of the study team, said: “In clinical settings, infections caused by M. abscessus are challenging to treat due to limited effective therapeutic options. These findings highlight the importance of anticipating how bacteria may respond to treatment. Strategies that account for such adaptive responses, including combination phage therapies, may enhance treatment durability, improve patient outcomes, and better inform clinical management of these complex infections.”
Advancing Novel Therapeutics and Diagnostics Against AMR
By revealing how phage resistance happens, and how it can be mitigated, this study strengthens the ongoing efforts to develop novel therapeutics against AMR.
The findings may also inform future diagnostic and monitoring approaches, such as tracking bacterial form changes and resistance-associated mutations. This could help clinicians tailor treatments and adjust therapeutic strategies more responsively.
Beyond immediate clinical applications, understanding how bacteria evolve under therapeutic pressure is important for infectious disease preparedness. Such insights can inform the design of new therapies that remain effective even as pathogens adapt.
The study contributes to Singapore’s efforts to strengthen capabilities in infectious diseases research and develop solutions to address emerging global health challenges.
– END –
Enclosed:
ANNEX A – Notes to Editor on Research Findings
______________________________________________________________________
About the Agency for Science, Technology and Research (A*STAR)
The Agency for Science, Technology and Research (A*STAR) is Singapore's lead public sector R&D agency. Through open innovation, we collaborate with our partners in both the public and private sectors to benefit the economy and society. As a Science and Technology Organisation, A*STAR bridges the gap between academia and industry. Our research creates economic growth and jobs for Singapore, and enhances lives by improving societal outcomes in healthcare, urban living, and sustainability. A*STAR plays a key role in nurturing scientific talent and leaders for the wider research community and industry. A*STAR’s R&D activities span biomedical sciences to physical sciences and engineering, with research entities primarily located in Biopolis and Fusionopolis. For ongoing news, visit www.a-star.edu.sg.
Follow us on
Facebook | LinkedIn | Instagram | YouTube | TikTok
About A*STAR Infectious Diseases Labs (A*STAR IDL)
A*STAR Infectious Diseases Labs (A*STAR IDL) was established in April 2021 with a mission to be a leading research institute of infectious diseases in antimicrobial resistance, respiratory and vector-borne diseases. A*STAR IDL brings together infectious diseases expertise from across multiple disciplines to drive cutting edge translational infectious diseases research to contribute to Singapore’s national preparedness and defence against the threat of emerging infections. Building upon a robust foundation of our strong biomedical research capabilities and complemented by our globally connected scientific network, A*STAR IDL aims to focus on innovative technologies in infectious disease detection, intervention and prevention with a pathway to impact on health and economic outcomes. https://www.a-star.edu.sg/idlabs
Follow us on
Facebook | LinkedIn | Instagram
Journal
Proceedings of the National Academy of Sciences
Method of Research
Experimental study
Subject of Research
Cells
Article Title
Smooth-to-rough morphotype switching, a mechanism of phage resistance in Mycobacterium abscessus
LA REVUE GAUCHE - Left Comment: Search results for BACTERIOPHAGE
